Gotta Poop? Why Not in the Potty?

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We have been trying to get my son potty trained for a while now. He is finally cooperating with us again. We have to use rewards to ensure he goes pee in his potty chair and most of the time it works. Of course he still has accidents, but that is what they are, accidents. EXCEPT when it comes to pooping. He has never pooped in the potty. I don't know why he refuses to poop in it! Today he pooped twice and he refused to go in the potty for it. Instead he tried to hide in corners and behind the sofa! I just have no clue as to why he does this. He has no problem peeing in it so what is the big problem with pooping in it? Has anyone had this happen with their kids? Anyone have any ideas about why he won't poop in the potty? We are absolutely baffled by it and I could really use any help at all.